Re: Discrepancy for the cluster ID's saved in state an available in GUI.Re: Discrepancy for the cluster ID's saved in state an available in GUI.Ok, I'm pretty sure there is a problem on your side. I tested this on
Windows Vista, Windows 7, Mac OS X 10.7, and two different Linux
systems. On one Linux system I tested it with Python 2.5, 2.6, and
2.7, using different wxPython 2.8 or 2.9 combinations. In all cases,
the 'model_cluster' entry was present in the drop-down menu. So I
selected that and the spin ":4@N" in the second element and clicked on
ok. Then in the prompt GUI window, I saw:
relax> cdp.clustering
{'free spins': [':5@N', ':6@N'], 'model_cluster': [':2@N', ':3@N', ':4@N']}
relax>
I could see this on all systems. Before the commit:
------------------------------------------------------------------------
r21219 | bugman | 2013-10-23 16:08:26 +0200 (Wed, 23 Oct 2013) | 7 lines
Changed paths:
M /branches/relax_disp/specific_analyses/relax_disp/api.py
Fix for the relaxation dispersion specific private _cluster_ids() method.
This was identified at
http://thread.gmane.org/gmane.science.nmr.relax.devel/4716.
The cluster data structure was not being referenced correctly.
------------------------------------------------------------------------
I could also not see 'model_cluster' in the drop-down menu, only 'free
spins', but after the change on all systems I can see both. So I
really cannot for the life of me work out why you cannot see
'model_cluster' in the drop-down menu :S
Regards,
Edward
On 23 October 2013 18:23, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
> I am on redhat linux.
>
> uname -a
> Linux haddock 2.6.32-358.18.1.el6.x86_64 #1 SMP Fri Aug 2 17:04:38 EDT 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
> in relax:
> import wx
> wx.__version__
> '2.8.12.0'
>
> ------------
> Hardware information:
> Machine: x86_64
> Processor: x86_64
> Endianness: little
> Total RAM size: 24013 Mb
> Total swap size: 26191 Mb
>
> Operating system information:
> System: Linux
> Release: 2.6.32-358.18.1.el6.x86_64
> Version: #1 SMP Fri Aug 2 17:04:38 EDT 2013
> GNU/Linux version: Red Hat Enterprise Linux Server 6.4 Santiago
> Distribution: redhat 6.4 Santiago
> Full platform string:
> Linux-2.6.32-358.18.1.el6.x86_64-x86_64-with-redhat-6.4-Santiago
>
> Python information:
> Architecture: 64bit ELF
> Python version: 2.6.6
> Python branch: tags/r266
> Python build: r266:84292, May 27 2013 05:35:12
> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-3)
> Libc version: glibc 2.2.5
> Python implementation: CPython
> Python revision: 84292
> Python executable: /usr/bin/python
> Python flags: sys.flags(debug=0, py3k_warning=0,
> division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
> Python float info: sys.floatinfo(max=1.7976931348623157e+308,
> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16,
> radix=2, rounds=1)
> Python module path: ['/sbinlab2/software/NMR-relax/relax_disp',
> '/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python',
> '/net/tomat/home/tlinnet/kte/t1rho_NCBD/Original_data/relax',
> '/sbinlab2/software/x64/haddock2.1',
> '/sbinlab2/software/x64/lib64/python2.6/site-packages',
> '/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/python', '/usr/lib64/python26.zip',
> '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2',
> '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old',
> '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages',
> '/usr/lib64/python2.6/site-packages/gst-0.10',
> '/usr/lib64/python2.6/site-packages/gtk-2.0',
> '/usr/lib64/python2.6/site-packages/webkit-1.0',
> '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode',
> '/usr/lib/python2.6/site-packages',
> '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info']
>
> Python packages and modules (most are optional):
>
> Name Installed Version Path
> minfx True 1.0.5
> /usr/lib/python2.6/site-packages/minfx
> bmrblib True 1.0.3
> /usr/lib/python2.6/site-packages/bmrblib
> numpy True 1.4.1
> /usr/lib64/python2.6/site-packages/numpy
> scipy True 0.7.2
> /usr/lib64/python2.6/site-packages/scipy
> wxPython True 2.8.12.0 (gtk2-unicode)
> /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx
> mpi4py True 1.3.1
> /usr/lib64/python2.6/site-packages/mpi4py
> epydoc False
> optparse True 1.5.3
> /usr/lib64/python2.6/optparse.pyc
> readline True
> /usr/lib64/python2.6/lib-dynload/readline.so
> profile True
> /usr/lib64/python2.6/profile.pyc
> bz2 True
> /usr/lib64/python2.6/lib-dynload/bz2.so
> gzip True
> /usr/lib64/python2.6/gzip.pyc
> io True
> /usr/lib64/python2.6/io.pyc
> xml True 0.8.4 (PyXML)
> /usr/lib64/python2.6/site-packages/_xmlplus/__init__.pyc
> xml.dom.minidom True
> /usr/lib64/python2.6/site-packages/_xmlplus/dom/minidom.pyc
>
> relax information:
> Version: repository checkout
> Processor fabric: Uni-processor.
>
> relax C modules:
>
> Module Compiled File type
> Path
> target_functions.relax_fit True ELF 64-bit LSB shared object,
> x86-64, version 1 (SYSV), dynamically linked, not stripped
> /sbinlab2/software/NMR-relax/relax_disp/target_functions/relax_fit.so
>
>
>
>
> 2013/10/23 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>>
>> Hmmm, very strange. I just repeated your steps and managed to add the
>> spin ":4" to 'model_cluster'. I cannot see the problem on my system.
>> Which OS are you on and which wxPython version are you using? I might
>> have to test this on a different OS!
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>> On 23 October 2013 18:04, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
>> wrote:
>> > Hi Edward.
>> >
>> > Version is:
>> > 21219
>> >
>> > If I do this in the prompt:
>> > --------
>> > pipe.create(pipe_name='test', bundle='test', pipe_type='relax_disp')
>> >
>> > spin.create(spin_name='N', spin_num=1, res_name='V', res_num=2,
>> > mol_name=None)
>> > spin.create(spin_name='N', spin_num=2, res_name='F', res_num=3,
>> > mol_name=None)
>> > spin.create(spin_name='N', spin_num=3, res_name='G', res_num=4,
>> > mol_name=None)
>> > spin.create(spin_name='N', spin_num=4, res_name='R', res_num=5,
>> > mol_name=None)
>> > spin.create(spin_name='N', spin_num=5, res_name='C', res_num=6,
>> > mol_name=None)
>> >
>> > relax_disp.cluster('model_cluster', ':2@N')
>> > relax_disp.cluster('model_cluster', ':3@N')
>> > ---------
>> >
>> > cdp.clustering
>> > {'free spins': [':4@N', ':5@N', ':6@N'], 'model_cluster': [':2@N',
>> > ':3@N']}
>> >
>> > Open Data Pipe Editor (Ctrl+d)
>> > Right click the pipe, and click "Associate with new auto-analysis".
>> >
>> > The "free spins, model_cluster" is in the line.
>> >
>> > But if I Click "Cluster button", I cannot assign new spin ids to
>> > 'model_cluster'
>> > since that label is not available in the dropdown.
>> >
>> >
>> > 2013/10/23 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >>
>> >> This is strange. In the relax_disp branch I started the GUI with:
>> >>
>> >> $ relax -g
>> >>
>> >> Then started a new dispersion analysis, opened the prompt window and
>> >> typed:
>> >>
>> >> relax> cdp.clustering = {
>> >> 'free spins': [':5@N', ':9@N', ':11@N', ':12@N', ':13@N', ':14@N',
>> >> ':25@N', ':31@N', ':33@N', ':39@N', ':42@N', ':80@N', ':87@N',
>> >> ':89@N', ':90@N', ':111@N', ':121@N'],
>> >> 'model_cluster': [':2@N', ':3@N', ':4@N', ':6@N', ':7@N', ':8@N',
>> >> ':10@N', ':15@N', ':16@N', ':17@N', ':18@N', ':19@N', ':20@N',
>> >> ':21@N', ':22@N', ':23@N', ':26@N', ':27@N', ':28@N', ':29@N',
>> >> ':30@N', ':32@N', ':34@N', ':35@N', ':36@N', ':37@N', ':38@N',
>> >> ':40@N', ':41@N', ':43@N', ':44@N', ':45@N', ':46@N', ':48@N',
>> >> ':49@N', ':50@N', ':51@N', ':52@N', ':54@N', ':55@N', ':56@N',
>> >> ':57@N', ':58@N', ':59@N', ':60@N', ':61@N', ':62@N', ':63@N',
>> >> ':64@N', ':65@N', ':66@N', ':67@N', ':68@N', ':72@N', ':73@N',
>> >> ':74@N', ':75@N', ':76@N', ':77@N', ':78@N', ':81@N', ':82@N',
>> >> ':83@N', ':84@N', ':85@N', ':91@N', ':92@N', ':93@N', ':94@N',
>> >> ':95@N', ':96@N', ':97@N', ':98@N', ':99@N', ':100@N', ':101@N',
>> >> ':104@N', ':105@N', ':106@N', ':107@N', ':109@N', ':110@N', ':112@N',
>> >> ':113@N', ':114@N', ':115@N', ':116@N', ':118@N', ':120@N', ':122@N',
>> >> ':123@N', ':124@N', ':125@N', ':127@N', ':129@N']
>> >> }
>> >>
>> >> Then when I click on the 'Cluster' button in the GUI, I can select
>> >> both the 'free spins' and 'model_cluster'. Maybe I was a bit fast
>> >> with the email. Could you update your code again, check that you have
>> >> r21219, and then see if the problem is still there?
>> >>
>> >> Cheers,
>> >>
>> >> Edward
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On 23 October 2013 17:24, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
>> >> wrote:
>> >> > Hi Edward.
>> >> >
>> >> > I still see the same behavior.
>> >> >
>> >> > Best
>> >> > Troels
>> >> >
>> >> >
>> >> > 2013/10/23 Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> >> >>
>> >> >> Hi Troels,
>> >> >>
>> >> >> This does look like it is an issue. I think I have located the
>> >> >> problem to the _cluster_ids() method in
>> >> >> specific_analyses/relax_disp/api.py. At least I fixed a bug in that
>> >> >> method. Could you check again to see if it is fixed?
>> >> >>
>> >> >> Cheers,
>> >> >>
>> >> >> Edward
>> >> >>
>> >> >>
>> >> >>
>> >> >> On 22 October 2013 19:34, Troels Emtekær Linnet
>> >> >> <tlinnet@xxxxxxxxxxxxx>
>> >> >> wrote:
>> >> >> > Hi Edward.
>> >> >> >
>> >> >> > Before I do a clustering analysis, I often prepare the data in
>> >> >> > scripts,
>> >> >> > save
>> >> >> > the state, and then
>> >> >> > inspect the setup in the GUI.
>> >> >> >
>> >> >> > I open the relax saved state.
>> >> >> > Open the Data Pipe Editor (Ctrl+d)
>> >> >> > Right click the pipe, and click "Associate with new
>> >> >> > auto-analysis".
>> >> >> >
>> >> >> > If I open the prompt (Ctrl+p), and write
>> >> >> > cdp.clustering
>> >> >> >
>> >> >> > I get
>> >> >> > {
>> >> >> > 'free spins': [':5@N', ':9@N', ':11@N', ':12@N', ':13@N', ':14@N',
>> >> >> > ':25@N',
>> >> >> > ':31@N', ':33@N', ':39@N', ':42@N', ':80@N', ':87@N', ':89@N',
>> >> >> > ':90@N',
>> >> >> > ':111@N', ':121@N'],
>> >> >> > 'model_cluster': [':2@N', ':3@N', ':4@N', ':6@N', ':7@N', ':8@N',
>> >> >> > ':10@N',
>> >> >> > ':15@N', ':16@N', ':17@N', ':18@N', ':19@N', ':20@N', ':21@N',
>> >> >> > ':22@N',
>> >> >> > ':23@N', ':26@N', ':27@N', ':28@N', ':29@N', ':30@N', ':32@N',
>> >> >> > ':34@N',
>> >> >> > ':35@N', ':36@N', ':37@N', ':38@N', ':40@N', ':41@N', ':43@N',
>> >> >> > ':44@N',
>> >> >> > ':45@N', ':46@N', ':48@N', ':49@N', ':50@N', ':51@N', ':52@N',
>> >> >> > ':54@N',
>> >> >> > ':55@N', ':56@N', ':57@N', ':58@N', ':59@N', ':60@N', ':61@N',
>> >> >> > ':62@N',
>> >> >> > ':63@N', ':64@N', ':65@N', ':66@N', ':67@N', ':68@N', ':72@N',
>> >> >> > ':73@N',
>> >> >> > ':74@N', ':75@N', ':76@N', ':77@N', ':78@N', ':81@N', ':82@N',
>> >> >> > ':83@N',
>> >> >> > ':84@N', ':85@N', ':91@N', ':92@N', ':93@N', ':94@N', ':95@N',
>> >> >> > ':96@N',
>> >> >> > ':97@N', ':98@N', ':99@N', ':100@N', ':101@N', ':104@N', ':105@N',
>> >> >> > ':106@N',
>> >> >> > ':107@N', ':109@N', ':110@N', ':112@N', ':113@N', ':114@N',
>> >> >> > ':115@N',
>> >> >> > ':116@N', ':118@N', ':120@N', ':122@N', ':123@N', ':124@N',
>> >> >> > ':125@N',
>> >> >> > ':127@N', ':129@N']
>> >> >> > }
>> >> >> >
>> >> >> > But if I click the "Cluster" button, The cluster ID
>> >> >> > "model_cluster'",
>> >> >> > is
>> >> >> > not
>> >> >> > available from the drop-down list.
>> >> >> >
>> >> >> > Should this be fixed?
>> >> >> >
>> >> >> > Best
>> >> >> > Troels
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > relax (http://www.nmr-relax.com)
>> >> >> >
>> >> >> > This is the relax-devel mailing list
>> >> >> > relax-devel@xxxxxxx
>> >> >> >
>> >> >> > To unsubscribe from this list, get a password
>> >> >> > reminder, or change your subscription options,
>> >> >> > visit the list information page at
>> >> >> > https://mail.gna.org/listinfo/relax-devel
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>